GapMind for catabolism of small carbon sources

 

Protein WP_101443868.1 in Pontibacter ramchanderi LP43

Annotation: NCBI__GCF_002846395.1:WP_101443868.1

Length: 241 amino acids

Source: GCF_002846395.1 in NCBI

Candidate for 62 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-arginine catabolism artP med Arginine transport ATP-binding protein ArtM (characterized) 40% 90% 152.1 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 58% 264.2
L-glutamate catabolism gltL med GluA aka CGL1950, component of Glutamate porter (characterized) 43% 84% 147.9 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 58% 264.2
L-histidine catabolism PA5503 lo Methionine import ATP-binding protein MetN 2, component of L-Histidine uptake porter, MetIQN (characterized) 37% 69% 155.6 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 58% 264.2
L-proline catabolism proV lo glycine betaine/l-proline transport atp-binding protein prov (characterized) 43% 50% 152.1 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 58% 264.2
L-lysine catabolism hisP lo ABC transporter for L-Lysine, ATPase component (characterized) 37% 94% 147.5 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 58% 264.2
L-asparagine catabolism glnQ lo Glutamine ABC transporter ATP-binding protein, component of Glutamine transporter, GlnQP. Takes up glutamine, asparagine and glutamate which compete for each other for binding both substrate and the transmembrane protein constituent of the system (Fulyani et al. 2015). Tandem substrate binding domains (SBDs) differ in substrate specificity and affinity, allowing cells to efficiently accumulate different amino acids via a single ABC transporter. Analysis revealed the roles of individual residues in determining the substrate affinity (characterized) 37% 89% 146.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 58% 264.2
L-asparagine catabolism bgtA lo ATPase (characterized, see rationale) 37% 91% 144.4 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 58% 264.2
L-aspartate catabolism bgtA lo ATPase (characterized, see rationale) 37% 91% 144.4 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 58% 264.2
D-sorbitol (glucitol) catabolism mtlK lo ABC transporter for D-Sorbitol, ATPase component (characterized) 38% 57% 144.1 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 58% 264.2
D-maltose catabolism thuK lo ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized) 38% 62% 141 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 58% 264.2
sucrose catabolism thuK lo ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized) 38% 62% 141 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 58% 264.2
trehalose catabolism thuK lo ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized) 38% 62% 141 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 58% 264.2
L-histidine catabolism hisP lo Histidine transport ATP-binding protein HisP (characterized) 38% 87% 140.2 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 58% 264.2
L-asparagine catabolism aatP lo ABC transporter for L-asparagine and L-glutamate, ATPase component (characterized) 35% 97% 139.8 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 58% 264.2
L-aspartate catabolism aatP lo ABC transporter for L-asparagine and L-glutamate, ATPase component (characterized) 35% 97% 139.8 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 58% 264.2
D-cellobiose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 37% 63% 139.8 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 58% 264.2
L-citrulline catabolism AO353_03040 lo ABC transporter for L-Arginine and L-Citrulline, ATPase component (characterized) 34% 92% 139.8 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 58% 264.2
D-galactose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 37% 63% 139.8 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 58% 264.2
D-glucose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 37% 63% 139.8 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 58% 264.2
lactose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 37% 63% 139.8 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 58% 264.2
D-maltose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 37% 63% 139.8 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 58% 264.2
D-mannose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 37% 63% 139.8 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 58% 264.2
sucrose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 37% 63% 139.8 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 58% 264.2
trehalose catabolism glcV lo monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized) 37% 63% 139.8 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 58% 264.2
xylitol catabolism Dshi_0546 lo ABC transporter for Xylitol, ATPase component (characterized) 37% 62% 138.3 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 58% 264.2
D-maltose catabolism malK1 lo MalK; aka Sugar ABC transporter, ATP-binding protein, component of The maltose, maltotriose, mannotetraose (MalE1)/maltose, maltotriose, trehalose (MalE2) porter (Nanavati et al., 2005). For MalG1 (823aas) and MalG2 (833aas), the C-terminal transmembrane domain with 6 putative TMSs is preceded by a single N-terminal TMS and a large (600 residue) hydrophilic region showing sequence similarity to MLP1 and 2 (9.A.14; e-12 & e-7) as well as other proteins (characterized) 33% 63% 136.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 58% 264.2
D-mannitol catabolism mtlK lo ABC transporter for D-mannitol and D-mannose, ATPase component (characterized) 36% 57% 134.8 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 58% 264.2
lactose catabolism lacK lo LacK, component of Lactose porter (characterized) 38% 58% 134 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 58% 264.2
L-proline catabolism opuBA lo BusAA, component of Uptake system for glycine-betaine (high affinity) and proline (low affinity) (OpuAA-OpuABC) or BusAA-ABC of Lactococcus lactis). BusAA, the ATPase subunit, has a C-terminal tandem cystathionine β-synthase (CBS) domain which is the cytoplasmic K+ sensor for osmotic stress (osmotic strength)while the BusABC subunit has the membrane and receptor domains fused to each other (Biemans-Oldehinkel et al., 2006; Mahmood et al., 2006; Gul et al. 2012). An N-terminal amphipathic α-helix of OpuA is necessary for high activity but is not critical for biogenesis or the ionic regulation of transport (characterized) 36% 54% 134 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 58% 264.2
L-arabinose catabolism xacJ lo Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale) 34% 55% 129.8 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 58% 264.2
L-tryptophan catabolism ecfA2 lo Energy-coupling factor transporter ATP-binding protein EcfA2; Short=ECF transporter A component EcfA2; EC 7.-.-.- (characterized, see rationale) 38% 77% 129.8 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 58% 264.2
L-histidine catabolism hutV lo ABC transporter for L-Histidine, ATPase component (characterized) 39% 75% 129 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 58% 264.2
L-arabinose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 35% 57% 128.6 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 58% 264.2
D-fructose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 35% 57% 128.6 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 58% 264.2
sucrose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 35% 57% 128.6 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 58% 264.2
D-xylose catabolism araV lo AraV, component of Arabinose, fructose, xylose porter (characterized) 35% 57% 128.6 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 58% 264.2
D-cellobiose catabolism gtsD lo ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 31% 59% 127.1 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 58% 264.2
D-galactose catabolism PfGW456L13_1897 lo ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 31% 59% 127.1 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 58% 264.2
D-glucose catabolism gtsD lo ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 31% 59% 127.1 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 58% 264.2
lactose catabolism gtsD lo ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 31% 59% 127.1 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 58% 264.2
D-maltose catabolism gtsD lo ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 31% 59% 127.1 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 58% 264.2
sucrose catabolism gtsD lo ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 31% 59% 127.1 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 58% 264.2
trehalose catabolism gtsD lo ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized) 31% 59% 127.1 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 58% 264.2
putrescine catabolism potA lo PotG aka B0855, component of Putrescine porter (characterized) 34% 62% 125.6 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 58% 264.2
trehalose catabolism malK lo MsmK aka SMU.882, component of The raffinose/stachyose transporter, MsmEFGK (MalK (3.A.1.1.27) can probably substitute for MsmK; Webb et al., 2008). This system may also transport melibiose, isomaltotriose and sucrose as well as isomaltosaccharides (characterized) 32% 59% 122.9 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 58% 264.2
D-cellobiose catabolism msiK lo MsiK protein, component of The cellobiose/cellotriose (and possibly higher cellooligosaccharides), CebEFGMsiK [MsiK functions to energize several ABC transporters including those for maltose/maltotriose and trehalose] (characterized) 32% 57% 122.5 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 58% 264.2
D-maltose catabolism musK lo ABC-type maltose transporter (EC 7.5.2.1) (characterized) 33% 57% 121.7 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 58% 264.2
D-maltose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 36% 58% 120.9 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 58% 264.2
sucrose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 36% 58% 120.9 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 58% 264.2
trehalose catabolism aglK lo ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized) 36% 58% 120.9 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 58% 264.2
D-maltose catabolism malK_Aa lo ABC-type maltose transporter (EC 7.5.2.1) (characterized) 31% 57% 119.8 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 58% 264.2
L-proline catabolism hutV lo HutV aka HISV aka R02702 aka SMC00670, component of Uptake system for hisitidine, proline, proline-betaine and glycine-betaine (characterized) 33% 85% 119.8 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 58% 264.2
D-cellobiose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 34% 56% 119 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 58% 264.2
D-glucose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 34% 56% 119 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 58% 264.2
lactose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 34% 56% 119 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 58% 264.2
D-maltose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 34% 56% 119 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 58% 264.2
sucrose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 34% 56% 119 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 58% 264.2
trehalose catabolism aglK' lo Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale) 34% 56% 119 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 58% 264.2
D-maltose catabolism malK_Sm lo MalK, component of Maltose/Maltotriose/maltodextrin (up to 7 glucose units) transporters MalXFGK (MsmK (3.A.1.1.28) can probably substitute for MalK; Webb et al., 2008) (characterized) 34% 59% 117.9 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 58% 264.2
D-cellobiose catabolism cbtD lo CbtD, component of Cellobiose and cellooligosaccharide porter (characterized) 34% 66% 115.9 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 58% 264.2
D-cellobiose catabolism TM0027 lo TM0027, component of β-glucoside porter (Conners et al., 2005). Binds cellobiose, laminaribiose (Nanavati et al. 2006). Regulated by cellobiose-responsive repressor BglR (characterized) 34% 89% 108.6 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 58% 264.2
glycerol catabolism glpS lo ABC transporter for Glycerol, ATPase component 1 (characterized) 35% 52% 100.5 Uncharacterized ABC transporter ATP-binding protein YknY; EC 7.6.2.- 58% 264.2

Sequence Analysis Tools

View WP_101443868.1 at NCBI

Find papers: PaperBLAST

Find functional residues: SitesBLAST

Search for conserved domains

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Predict transmenbrane helices: Phobius

Predict protein localization: PSORTb

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Sequence

MSTIIETNDISKVYRMGSETIHALKSVSIRIERGEYVAFMGPSGSGKSTLMNIIGCLDTP
TGGQYILNGQDVSNMTDNELAEVRNKEIGFVFQTFNLLPRQTSLENVALPLIYAGYNKSA
REEKAQKALESVGLGNRGKHKPNELSGGQRQRVAIARALINDPSIILADEPTGNLDTKTS
YEIMELFENLHAKGNTIIMVTHEEDIAKYAHRIVRLRDGLVESDEMNHDVTSHAGINAAQ
H

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory